Wheat to eatAccelerating plant breeding to address global food & nutrition security

Alison Bentley & the CIMMYT Global Wheat Program

IWGSC Webinar - 24th September 2021

a.bentley@cgiar.org

Wheat is essential to global food security

Global wheat area ~220 million ha

Developing countries

Developed countries

105 million

ha

115 million

ha

Average farm size: 1-3 ha vs. 40-5000 ha

A vast array of available breeding tools & resources

Genetic resources Elite germplasm Multi-environments Phenotyping methods Remote sensing

Marker-assisted selection

Pan-genomes Quality traits Biotechnology Genomic selection

Panel evaluation

Genotyping

Genetic mapping

Phenotyping

Donor identification

Challenge: how to funnel multiple outputs into breeding improvements?

Trait-linked markersInternational germplasm evaluation

Cd Obregon High yield (irrigated)Water-use efficiencyHeat toleranceLeaf rustStem rust (not Ug99)

TolucaYellow rust Septoria triticiFusariumZero tillage

El BatanLeaf rustFusarium

Njoro, KenyaStem rust (Ug99 group)Yellow rust

from Lantican, 2016

Context: achieving large impact worldwide through provision of improved germplasm from centralized breeding.

Continuous breeding progress for grain yield

Crespo-Herrera et al. (2021) Target population of environments for wheat breeding in India: definition, prediction and indirect genetic gains. Frontiers in Plant Science doi: 10.3389/fpls.2021.638520

2001–2016 across Indian TPEs1965–2014 in simulated environments (Cd. Obregón)

Mondal et al. (2020) Fifty years of semi-dwarf spring wheat breeding at CIMMYT: Grain yield progress in optimum, drought and heat stress environments. Field Crops Research doi: 10.1016/j.fcr.2020.107757.

Accelerating genetic gains in wheat breeding

• Faster breeding: new screenhouse infrastructure in Toluca is being used to reduce breeding cycle time from ~6 to 3 years per cycle

• Innovative methods: genomic selection is being implemented for rapid recycling of parents.

• Novel trait introgression: speed breeding has been initiated for rapid trait introgressions of race-specific genes and QTLs for disease resistance into elite lines.

6 Jan 2021

15 Jan 2021w/growth-enhancing

lights

5 Feb 2021Flowering / crossing

Adoption of rapid-generation breeding methods to reduce breeding cycle time

AGG-Wheat simulations led by FH Toledo

First cycle of crossing complete (August, 2021)

AGG-Wheat breeding scheme optimization led by Suchismita Mondal

DiscoveryNew donors, new genetic

variants

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1-2

year

s---

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Parental Selection

Phenotyping

F1

BC1

F1

BC2

F1

F2

F3

F4

Marker-assisted RGA

Seed increase

Line augmentation

Panel evaluation

Diversity panels

Support Services: New database structures, genotyping, decision support tools

Trait-pipeline activities toolkit

Parent development Marker design variant

introgression

Assess current pipeline demand, initiation of trait advances and augmentation (internal and external), future pipeline demand

Variant deployment, Product development

Marker-assisted trait development pipelines

Donor identification

Genotyping

Genetic mapping

Trait-pipeline advancement process

Parent developmentProduct augmentation

Accuracy of selection in segregating generations

Advancement in early-stage yield testing

Recycling parentsPopulation improvement

Large-effect genes/QTL known

Gene discovery and validation phase

NOYES

Gene/QTL deployment via

MABC or forward breeding

Trait pipeline (speed breeding)

Trait variation for pre-breeding

NO

Validated pre-breeding germplasm

Genomic- &/or phenotypic-assisted pre-

breeding

NO

Populations amenable to genomic selection

Genomic Selection

Crop* Project Value Product Profile Trait Genes

BWImproved and diversified rust resistance

HW-OE-NM, HW-DT-NM

Stem and yellow rust Sr22, Sr50, Sr2, Yr57, Yr59, Sr35, Yr15, Yr5, Sr47, Sr25, Sr13, YrSP

BWEnhanced Fhb resistance

HW-OE-NM, HW-DT-NM

Fusarium head blight Fhb1, Qfhb.cim-2DLc

BWImproved STB resistance

HW-OE-NM, HW-DT-NM Septoria tritici Blotch Stb6, Stb16

BW Improved insect resistance

HW-OE-NM, HW-DT-NM

Green bug Gb7/Gba, Gb5, QRp.slu-5AL, QRp.slu-5BL-R

BWNovel diversity for stress tolerance (heat drought)

- Heat/drought tolerance

LTP haplotypes from genetic resources (six haplotypes)

DWNovel stem rust resistance gene combinations

ADW-DT+IR, ADW-HTEM Stem rust Sr22 + Sr25

DW Improved grain weight/yield

ADW-DT+IR, ADW-HTEM Grain weight TaGW2

Current line augmentation pipelines

AGG-Wheat marker-trait introgression from Susanne Dreisigacker & Suchismita Mondal

Crop* BW = bread wheat; DW = durum wheat

Genotyping workflow

Sampling of leave tissue in the field or greenhouse

Genotyping

From sampling to data analysis

Project planning and genotyping preparation (sample managing and tracking)

Genotyping service

Data storage

DNA extraction

Sample shipment when outsourcing

Field selection based on MAS and phenotypic data

Data QC anddecision support tools

CIMMYT Wheat Molecular Biology lab led by Susanne Dreisigacker

Synthetic wheat Major QTL on chr7B Breeding marker Gene pyramiding

Native genetics for insect resistance

Current pyramiding of four loci in a single background using speed breeding & MAS

Aphid resistance work led by Leo Crespo & Susanne Dreisigacker

• Three-way crossing scheme of linked top-cross populations (LTP) in the Seed of Discovery project

Novel genomic regions derived from genetic resources

• Exotic parents include synthetic hexaploidy and landraces selected via FIGS

• Elite parent include lines from the spring BW breeding program

LTP discovery work led by Deepmala Sehgal & Susanne Dreisigacker

Quantification of the contribution of the exotic parents in LTPs

Genetic diversity of three LTP populations used for genetic analysis (2,867 pre-breeding lines)

Haplotype map of the exotic genome contribution to the pre-breeding lines (approx. 17%)

LTP1LTP2LTP3

1A 1B 1D 2A 2B 2D 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D 7A 7B 7D

Introgressed genomic regions from exotics are shown as red bars

LTP discovery work led by Deepmala Sehgal & Susanne Dreisigacker

0

500

1000

1500

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2500

GT AC GC

Heat-LTP1-YLD-15-16 Heat-LTP1-YLD-16-17

HB6D-Heat stress

0

500

1000

1500

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2500

AG TA

HB3B-Heat stress

GY

(+240-370 kg/ha in GY under heat stress)

(+176-326 kg/ha in GY under heat stress)

GY

Exotic-specific association derived by GWAS

Exotic specific associations

Haplotype frequencies in exotic parents and 16K genebank accessions

Evaluation & introgression of exotic-specific associations in elite backgrounds

Heat stress-3B Multiple stress-4B

Multiple stress-5B Multiple stress-7D-1 Multiple stress-7D-2

Heat stress-6D

Selected donor parents are

• Evaluated in additional yield and physiological trials

• Integrated in the breeders conventional crossing block

• Integrated in trait improvement pipelines for accelerated trait augmentation in elite germplasm

Catalogue of QTLs aligned to the wheat reference genome

CIMMYT QTL catalogue led by Deepmala Sehgal

From QTLs to haplotypes

In collaboration with Uauy group, John Innes Centre

https://www.cimmyt.org/news/cimmyt-and-john-innes-centre-announce-strategic-collaboration-on-wheat-research/

Mid-density, low-cost genotyping service platformPanel optimization: second design phase , maximizing overall SNPs

DArTAG – wheat panel vs. 02• A total of 3900 SNPs.• Includes more gene and QTL related sequences

(469), full QC marker set (125), in CIMMYT germplasm highly polymorphic, genome-wide distributed SNPs (1802)

• Connectivity to the KSU exome sequence capture platform (500 common SNPs)

• Connectivitiy to the ongoing development of UK Axiom Breeders Chip/s (1005 common SNPs)

Genome distribution of the 3900 SNP in DArTAG – wheat panel vs 02.

DArTAG wheat development led by Susanne Dreisigacker

But what about nutrition?

Selection for Zn in all CIMMYT wheat breeding pipelines to address malnutrition

https://www.reuters.com/business/healthcare-pharmaceuticals/exclusive-new-zinc-fortified-wheat-set-global-expansion-combat-malnutrition-2021-04-15/

Mainstreaming micronutrient biofortification

Yield gain progress for Zinc breeding pipeline

• HarvestPlus Yield Trial material produced by CIMMYT.

• Data analysed across international environments from 2010-2020.

• Annual yield gain of 0.755% and grain yield progress of 109 kg/ha/yr

• Yield gains are on par with core breeding material, whilst also having > 6 ppm average Zn increase.

Zn breeding led by Velu Govindan

Zn mainstreaming: assessment in Stage 1 BW materials (1500 lines)

0

10

20

30

40

50

60

<30 31-33 34-39 40-42 43-45 46-48 49-51 52-54 55-57

% E

ntr

ies

Grain Fe and Zn (ppm)

Fe Zn

Zn FeAv 43.43 39.34

Min 33.04 29.35Max 59.11 48.90

Ninga: 40 ppmBorlaug100: 44 ppm

Variation for Zn in core breeding pipelines

Zn breeding led by Velu Govindan

Effect of the bread production process on micronutrient retention using biofortified wheat

On-going study

Fundamental to understand efficacy of biofortification and impact of wheat processing on nutritional value

Zn processing studies led by Maria Itria Ibba

IH G

FE D

CB A

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10

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70

Flour Bread Chapati Flour Bread Chapati Flour Bread Chapati

70% 85% 100%

Zn C

once

ntra

tion

(mg/

g)-40%

-30%

Grain and flour processing & Zn concentration

• Significant reduction starting from 85% extraction rate• Bread or chapati production does NOT negatively affect Zn concentration

Zn processing studies led by Maria Itria Ibba

Improvement of wheat grain fiber (Arabinoxylan) content

Current research focused on:

1. Identification of germplasm associated with improved grain fiber content

2. Development of tools to facilitate the selection of high-fiber wheat lines

3. Understanding the environmental effect on grain fiber content variation

4. Understanding the effect of the arabinoxylan content variation on wheat quality

Results of these studies could potentially lead to an increased daily consumption of

dietary fibers

Hernandez-Espinosa et al., 2020. https://doi.org/10.1016/j.jcs.2020.103062; Ibba et al., 2021. https://doi.org/10.1016/j.jcs.2021.103166

Arabinoxylan studies led by Maria Itria Ibba

~ 190 hard spring common wheat lines

(2018/2019)

Wheat quality analysis

TOT- and WE-AX analysis(2 reps)

GWAS

Arabinoxylan studies led by Maria Itria Ibba

Increasing dietary fiber

Use in breeding: reliable molecular markers developed and are being applied to evaluate CIMMYT breeding lines.

From discovery to breeding application: CIMMYT has identified genetic regions increasing dietary fiber

Discovery: a large effect genetic region was identified that enhanced arabinoxylan content

Validation: the identified region clearly distinguishes elite lines showing low or high contents.

Arabinoxylan studies led by Maria Itria Ibba

Selection for wholemeal bread qualityAre we using the best methods to predict lines with high “healthy” breakmaking potential?

Experiments conducted using full quality characterization and using three bread making procedures:

• Classic (refined flour and 1g NaCl)• Low sodium (refined flour and no added salt)• Wholemeal (Reconstituted flour and 1g NaCl)

AB

C

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RF RNa WM

Lo

af

vo

lum

e (

mL

)

AB

C

0

0.5

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1.5

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RF RNa WM

Cru

mb

sco

re

Hernández-Espinosa et al. (2021) https://doi.org/10.1002/cche.10457

Comparing bread loaf volumes

R² = 0.8064

R² = 0.4045

350

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550 600 650 700 750 800 850

LV

-WM

an

d L

V-R

Na (

mL

)

LV-RF and LV-WM (mL)

LV-RF vs LV-RNa LV-RF vs LV-WM

LV=Loaf volume; RF=Refined flour; RNa=Reduced sodium; WM=Wholemeal

Main findings: • Current standard protocols can

be used effectively to select high-quality low-sodium breads

• Current standard protocols can be used to estimate the wholemeal breadmaking quality

Hernández-Espinosa et al. (2021) https://doi.org/10.1002/cche.10457

Equitably deploying breeding tools & resources

Genetic resources Elite germplasm Multi-environments Phenotyping methods Remote sensing

Marker-assisted selection

Pan-genomes Quality traits Biotechnology Genomic selection

Find out more about the CIMMYT Global Wheat Program and our donors & partners: https://www.cimmyt.org/work/wheat-research/

https://wheat.org/

Accelerating Genetics Gains in Wheat (https://www.cimmyt.org/projects/agg/) is supported by the Bill & Melinda Gates Foundation, UK Foreign & Commonwealth Development Office, USAID and the

Foundation for Food and Agricultural Research